SZYBKI 1.5.2 (October 2010)

New features

  • Entropy calculation of protein-bound ligands has been modified. Specifically, the fraction \(f\) of ligand surface exposed to the solvent used in the entropy component term: \(f\Delta S_s\), is calculated currently as \(f = A_{Lexp}/A_L\), where \(A_{Lexp}\) and \(A_L\) are ligand solvent accessible surfaces in the protein complex and solution respectively. The reason for a change is the recent OpenEye internal study which show that the above fraction \(f\) calculated according to the equation: \(f = 0.5(A_L - A_P + A_{PL})/A_L\) ([Wlodek-2010]) is for many protein-ligand complexes overestimated. The previous way of protein-bound ligands entropy calculation is available with the option: “-ent 151”.
  • The default value of microscopic surface tension used for protein entropy desolvation calculation is now 6 \(cal/(mol A^2)\) (previously default value was set at 5 \(cal/(mol A^2)\). The flag “-sfp x”, where x is microscopic surface tension for protein desolvation entropy calculation, allows to overwrite the default value.
  • Two more flags have been introduced: “-t x” and “-rws”. The first of them sets the temperature x in C for entropy calculations (the default value is 25C). The second flag removes water molecules from all solvent accessible surface calculations used for the evaluation of protein-bound ligand entropy, in the case the input protein contains water molecules.
  • More entropy terms are reported in the log file. In earlier SZYBKI versions only the total entropy was reported. Starting from 1.5.2 release in addition to total entropy, configurational, solvation (or partial solvation) and protein desolvation entropy terms are reported.